Multi-Omics and Molecular Simulations Identify Orthosiphon aristatus Phytochemicals with Predicted Activity Against Tuberculosis via SRC Kinase Modulation as Host-Directed Therapy

Vollständiger Abstract

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Introduction: Tuberculosis (TB) remains a leading global health emergency, exacerbated by the rise of drug-resistant strains that reduce the efficacy of conventional treatments. Amid these challenges, there is a critical need for plant-derived host-directed therapies that can serve as adjuvants to current regimens. Orthosiphon aristatus, known as cat’s whiskers, is widely used in Indonesian traditional medicine and offers a rich phytochemical repertoire with unexplored therapeutic potential. However, its specific molecular targets against TB remain uncharacterized. This study addresses this gap by employing integrated multi-omics and molecular simulation approaches to identify bioactive phytochemicals in O. aristatus and predict their mechanisms of action against tuberculosis. Methods: An aqueous leaf extract was analyzed by Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) to identify its metabolite compounds. The predicted metabolite targets were integrated with tuberculosis-related genes using network pharmacology to pinpoint key regulatory hubs. Structure-based molecular docking was performed against the prioritized target SRC, followed by molecular dynamics simulations and MM/PBSA binding free-energy assessments to evaluate complex stability and interaction details. Results: LC-MS/MS analysis revealed a diverse metabolite profile comprising phenolic acids, flavonoids, alkaloids, fatty acids, and triterpenoids; representative signals included tartaric acid, adenosine, cyanidin-3-glucoside, chlorogenic acid, ethyl gallate, rosmarinic acid, acacetin, tetrahydropalmatine, solanidine, 16-hydroxyhexadecanoic acid, and dammarenediol. Network integration of tuberculosis disease targets and predicted metabolite targets yielded 194 overlaps and prioritized a kinase-centered module, with SRC as the highest-ranked hub, motivating receptor-focused screening. Structure-based docking against SRC highlighted three candidates with sub-micromolar predictions, namely solanidine (ΔG −9.69 kcal/mol; Ki ≈ 79.43 nM), dammarenediol (ΔG −9.13 kcal/mol; Ki ≈ 204.32 nM), and rubijervine (ΔG −9.00 kcal/mol; Ki ≈ 251.71 nM). One-hundred-nanosecond molecular dynamics simulations supported stable complexes for all three ligands with native-like backbone deviation, compactness consistent with deep burial for dammarenediol, and balanced solvation around rubijervine. Hydrogen-bond occupancy mapped recurring anchoring residues at MET344, LYS298, THR341, GLU342, and ASP407, while MM/PBSA decomposition indicated dispersion-driven binding with total energies of −71.866 ± 48.633 kJ/mol for solanidine, −69.077 ± 77.772 kJ/mol for dammarenediol, and −20.188 ± 56.455 kJ/mol for rubijervine. Discussion: The integrative in silico study highlights SRC as a key host-directed target that may be modulated by O. aristatus phytochemicals. Conclusion: This integrative multi-omics and molecular simulation study identifies solanidine and dammarenediol as leading SRC-targeted antituberculosis candidates from Orthosiphon aristatus and designates rubijervine as a distinct hinge-stabilizing scaffold. These findings establish a mechanistic foundation for the next phase of development, which will use enzymatic inhibition assays and macrophage infection models to validate the therapeutic index of these compounds. Ultimately, these findings represent a promising pathway for developing plant-derived adjunct therapies to combat drug-resistant tuberculosis.